I thought the Shoot reunion was appropriate for the characters. Of course those two would quickly escalate to a suicide stand-off as soon as they saw each other again. They have each been ready to sacrifice themselves for the other since Shaw ran into gunfire to allow the others to escape in the elevator. Shaw killed herself in 7000 simulations to avoid killing Root. And Root has been using her own life as collateral to play chicken with the Machine to try to find Shaw for a year, starting with her walk on a windy ledge that led to their trip to the asylum. We saw in Root's butter-churning and ballerina identities that she has never stopped asking the Machine to find Shaw for her, and she was more than willing to blow her own cover to push the Machine into action. Samaritan wasn't able to turn Shaw, but it was (maybe inadvertently) successful in conditioning her to blow her own brains out if she ever ran into Team Machine again. The only reason that it didn't work is that Root has been inadvertently conditioning herself to immediately put her own life at risk to save Shaw without wasting much time on any less-drastic options.
The fact that Samaritan never once guessed that Root would do that to save Shaw is a prime example of how Samaritan just doesn't get it. Because Samaritan sees every life as irrelevant and replaceable, no one is worth sacrificing anything for. Samaritan doesn't understand loyalty or sacrifice even after watching Shaw commit suicide 7000 times because it doesn't understand the value of life. Harold taught the Machine the value of life so well that it was willing to sacrifice itself for Harold and Root in the season 4 finale. It recruits killers like Root, Shaw, and John to do its bidding, but each of them demonstrated a deep loyalty and attachment to someone they would risk danger to avenge (Root's friend Hannah, Shaw's partner, Jessica) even before the Machine brought them into the team. And they all, especially Root, have a stronger appreciation of human life since they began working with the Machine.